DNA metabarcoding generates robust, replicable biodiversity data at unprecedented scales. This data can be used to inform crucial environmental management decisions.
Metabarcoding is a method of sequencing the DNA barcodes of many different organisms in parallel. Metabarcoding uses High Throughput Sequencing on community DNA to identify diverse taxa in a single reaction. When metabarcoding is applied to environmental samples, such as water, it is known as ‘eDNA metabarcoding’.
How does metabarcoding compare with classic DNA barcoding? Although we use classic DNA barcoding for some things, for example when building reference databases, it is of limited use for biodiversity surveys for two main reasons. First, classic barcoding is too slow and expensive for generating large-scale data across diverse groups (e.g. arthropods other invertebrates) because it requires a separate sequencing reaction for each specimen. Second, classic barcoding can’t be used on samples that contain DNA from a mixture of related species (e.g. environmental samples). This is why we use metabarcoding to bypass these limitations when generating large scale biodiversity data.
The principal steps in a metabarcoding pipeline are:
- Extract community DNA from your sample. If you are working with bulk samples of invertebrates, this includes a homogenisation (blending) step prior to DNA extraction.
- Amplify a barcode region using primers optimised for your target taxon group (e.g. fish / arthropods / molluscs). This makes millions of copies of the barcode gene in preparation for sequencing.
- Sequence the amplified DNA on a high throughput sequencing platform such as the Illumina MiSeq, which generates around 30 million sequences in around 2.5 days.
- Bioinformatically process the raw sequence data to obtain a species x sample table that can be used for ecological analysis